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Bernhard Bein

@bernhardbein.bsky.social

29 followers 59 following 13 posts

PhD student in comparative genomics @ Senckenberg and Goethe University Frankfurt

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Bernhard Bein @bernhardbein.bsky.social · Feb 10

Thrilled to share our work on unlocking challenging specimens for @pacbio.bsky.social #HiFi sequencing, now out in Genome Biology!

genomebiology.biomedcentral.com/articles/10....

We show that specimens that have been stored in ethanol for decades can still be amenable for long-read sequencing:🧵

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens - Genome Biology

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protoco...

genomebiology.biomedcentral.com

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Reposted by Bernhard Bein

Marcela Uliano-Silva @marcelauliano.bsky.social · 6d

Preprint Alert! 🦥
We produced complete genomes for 2 Xenarthra and placed them in a mammalian comparative framework. We found that Xenarthra harbour the largest number of retrocopies in mammals! www.biorxiv.org/content/10.1...

Retrocopy formation and domestication shape genome evolution in sloths and other xenarthrans

Xenarthrans, comprising sloths, anteaters, and armadillos, represent one of the most morphologically and physiologically specialised mammalian clades, yet the genomic basis of their adaptations remain...

www.biorxiv.org

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Reposted by Bernhard Bein

Adam Phillippy @aphillippy.bsky.social · 16d

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

www.biorxiv.org

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Reposted by Bernhard Bein

Adam Ameur @adameur.bsky.social · 28d

New preprint! With PureTarget we achieved >1000× coverage of targets with ~5kb PacBio reads at QV39. This enabled high-resolution analysis of CRISPR-Cas9 outcomes

Key finding: Some CRISPR-mutations may only emerge in the second generation, due to germ cell mosaicism

www.biorxiv.org/content/10.1...

Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads

Background: Genetic mosaicism is a consequence of CRISPR-Cas9 genome editing that is difficult to study, especially when it involves structural variants occurring at low frequency. A comprehensive ana...

www.biorxiv.org

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Reposted by Bernhard Bein

Nature @nature.com · Sep 3

A common type of ant in Europe breaks a fundamental rule in biology: its queens can produce male offspring that are a whole different species

go.nature.com/4mOb5T9

‘Almost unimaginable’: these ants are different species but share a mother

Ant queens of one species clone ants of another to create hybrid workers that do their bidding.

go.nature.com

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Bernhard Bein @bernhardbein.bsky.social · Sep 3

#PacBio #ULI #HiFi sequencing goes clinical:

Really cool paper showing that Ultra-low input (ULI) HiFi sequencing can help cancer diagnostics.
Only emphasizes how interdisciplinary the ULI field is ( #museomics, #single-cell #sequencing, #diagnostics etc)

www.medrxiv.org/content/10.1...

Whole-genome variant detection in long-read sequencing data from ultra-low input patient samples

Long-read sequencing provides a more complete view of the genome than short-read sequencing, with advantages in the detection of structural variants, tandem repeats, and small variants (single nucleot...

www.medrxiv.org

Reposted by Bernhard Bein

Xueling (Ling) Yi @xuelingyi.bsky.social · Aug 19

The poster session was really great and lots of fun @eseb2025.bsky.social! Many interesting discussions and ideas! Thanks to everyone who stopped by at my poster! Looking forward to more interesting talks and posters in the following days!

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Reposted by Bernhard Bein

Vertebrate Genomes Project @vertebrategenomes.bsky.social · Jul 30

🔗 https://doi.org/10.1093/bioinformatics/btaf416
💻️ rdeval code: https://github.com/vgl-hub/rdeval (3/3)

GitHub - vgl-hub/rdeval: Multithreaded read analysis

Multithreaded read analysis. Contribute to vgl-hub/rdeval development by creating an account on GitHub.

github.com

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Reposted by Bernhard Bein

Leon Hilgers @leonhilgers.bsky.social · Jul 24

You link #phenotype 🦜 to #genotype 🧬 with #comparative #genomics 💻?

This #review is for you 📜: authors.elsevier.com/sd/article/S...

We review new #methods, remaining #challenges and #future directions and highlight recent key studies.

Thanks @hillermich.bsky.social!

Please share! 🙂

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Reposted by Bernhard Bein

mara lawniczak @marakat.bsky.social · Jul 7

new from the lab -- we investigate 100% ethanol, DMSO salt solution (DESS), EDTA, RNAlater, and AllProtect as possible approaches for short term room temperature preservation of mosquito HMW DNA, nuclei for Hi-C, and RNA towards high quality reference genome creation. the key findings/tips are ....

bioRxiv Genomics @biorxiv-genomic.bsky.social · Jul 6

Breaking the cold chain: solutions for room temperature preservation of mosquitoes leading to high quality reference genomes https://www.biorxiv.org/content/10.1101/2025.07.03.662936v1

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Bernhard Bein @bernhardbein.bsky.social · Jul 6

6 years ago, a dream came true when Chao took me along on a field trip to look for freshwater crabs in Guangdong. Now, the new species we found is formally described (𝘔𝘦𝘨𝘢𝘱𝘭𝘦𝘰𝘯𝘶𝘮 𝘺𝘢𝘯𝘨𝘥𝘰𝘯𝘨𝘦𝘯𝘴𝘦 in the article).
Congrats!!

zookeys.pensoft.net/articles.php...

#FreshwaterCrab #Biodiversity #Potamidae

Four new freshwater crab species of the genus Megapleonum Huang, Shih & Ahyong, 2018 (Crustacea, Decapoda, Potamidae) from Guangdong, China

Four new species of the poorly known genus Megapleonum Huang, Shih & Ahyong, 2018, are described from Guangdong Province, China: Megapleonum falx sp. nov. from Huizhou City, M. yangdongense sp. no...

zookeys.pensoft.net

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Reposted by Bernhard Bein

Phil Morin @philmor1964.bsky.social · Jul 3

The Cetacean Genomes Project is happy to share a milestone publication, presenting the first 18 reference-quality, chromosome-resolved genomes of whales, dolphins and porpoises across the cetacean tree of life. www.frontiersin.org/journals/mar...

Frontiers | Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life

Reference genomes from representative species across families provide the critical infrastructure for research and conservation. The Cetacean Genomes Project...

www.frontiersin.org

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Bernhard Bein @bernhardbein.bsky.social · May 20

Exciting news! Good to see that findings from our study on ethanol-preserved specimens are now applied to formalin-fixed cancer samples. Looking forward to more of these interdisciplinary applications regarding amplification-aided sequencing (i. e. scWGA).

#PCRAmplification #LongReadSequencing

PacBio @pacbio.bsky.social · May 19

Back in January, over 5,000 people explored our blog introducing Ampli-Fi.

Now, we’re sharing how this protocol is helping bring #HiFisequencing to FFPE samples in cancer research.

🔗 Read the update: bit.ly/4dkvkDO

#PacBio #CancerResearch

Cancer research gains a powerful new tool as Ampli-Fi makes HiFi sequencing possible for FFPE-preserved samples - PacBio

Cancer research depends on the details we can actually see. And, until now, FFPE samples have not been compatible with long-read sequencing. That’s changing. This year at AACR, we...

bit.ly

Reposted by Bernhard Bein

ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · Apr 23

#ERGAReads | Thinking of sequencing a genome in your lab? 🧬 This review offers practical guidance on how to start a #genome project for non-model species - covering DNA extraction, sequencing tech, costs, and more!

🔗 rdcu.be/eiHRG

@sgn.one @leibnizlib.bsky.social #biodiversity #genomics

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Reposted by Bernhard Bein

Carola Greve @cgreve.bsky.social · Apr 17

Still no reading material for the Easter break🌞🌻🐰? Then I have a suggestion: "Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide" (lnkd.in/dsRmSBDE). It was a pleasure to work on this new publication with TilmanSchell & @lpodsiadlowski.bsky.social🙏!

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Bernhard Bein @bernhardbein.bsky.social · Mar 21

Research about ultra-low input DNA seq and MDA I recently found:

1. MDA on pg input DNA for ONT rapid seq of pathogens + Tool to detect concatemers
doi.org/10.1111/1755...

2. MDA for metagenomics of low biomass samples
doi.org/10.1093/isme...

Exciting Stuff, small inputs + ampli. going strong!

Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing

Multiple displacement amplification (MDA) outperforms conventional PCR in long fragment and whole-genome amplification, making it attractive to couple MDA with long-read sequencing of samples with li...

onlinelibrary.wiley.com

Reposted by Bernhard Bein

Senckenberg Gesellschaft für Naturforschung @sgn.one · Mar 3

🐙 Jetzt abstimmen: Molluske des Jahres 2025! 🐌
5 beeindruckende Weichtiere stehen im Finale. Dem Gewinner-Weichtier winkt die Entschlüsselung seines kompletten Genoms! 🧬🏆

Erfahrt mehr über die Kandidaten und stimmt bis zum 31.3. für euren Favoriten ab 👉 moty.senckenberg.science

Ein Kraken der Gattung Muusoctopus schwimmt am Meeresgrund

Ein Blauer Drache (Glaucus atlanticus), eine leuchtend blaue Meeresnacktschnecke, schwebt in dunklem Wasser. Seine fingerartigen Fortsätze erstrecken sich symmetrisch vom Körper. Darunter ist eine blau-weiße, kreisförmige Kolonie einer Staatsqualle zu sehen.

Eine Hawaiische Schwarzfuß-Napfschnecke (Cellana exarata) guckt mit ausgestreckten Fühlern aus ihrer Muschelschale heraus, die auf sandigem Boden nahe einer dunklen Felswand liegt.

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Reposted by Bernhard Bein

Senckenberg Ocean Species Alliance (SOSA) @oceanspecies.bsky.social · Feb 28

𝗖𝗿𝗮𝗰𝗸𝗶𝗻𝗴 𝘁𝗵𝗲 𝗠𝗼𝗹𝗹𝘂𝘀𝗰 𝗖𝗼𝗱𝗲: A ground-breaking study in @science.org unravels the evolutionary history of molluscs: tinyurl.com/MolluscTree

@sgn.one @sigwartae.bsky.social @kmkocot.bsky.social @squamiferum.bsky.social @vans-gonzalez.bsky.social @cgreve.bsky.social @mkyapchiongco.bsky.social

A genome-based phylogeny for Mollusca is concordant with fossils and morphology

Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups—gastropods, bivalves, and cephalopods—e...

tinyurl.com

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Bernhard Bein @bernhardbein.bsky.social · Feb 24

This looks extremely promising and it works with smallish amounts of input DNA. Why? Because it applies long range PCR amplification with 'polC' (KOD Xtreme™ Hot Start DNA polymerase) that we investigated in depth here:

genomebiology.biomedcentral.com/articles/10....

#PacBio
#HiFiSequencing
#PCR

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Reposted by Bernhard Bein

KamilSJaron.bsky.social @kamilsjaron.bsky.social · Feb 14

With @katiejenike.bsky.social and a bunch more of our fellow k-mer enthusiasts, we put together a manuscript on k-mers in biodiversity genomics. A guide if you will, that covers k-mers from basics to some really funky stuff...

genome.cshlp.org/content/35/2...

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Bernhard Bein @bernhardbein.bsky.social · Feb 10

Huge thanks to the whole team, especially @hillermich.bsky.social @cmazzoni.bsky.social @astridboehne.bsky.social Sylke Winkler, Carola Greve,
@yanischrysost.bsky.social Larissa Arantes, Tom Brown, Charlotte Gerheim, Tilman Schell !!!

Bernhard Bein @bernhardbein.bsky.social · Feb 10

Based on our and another study, @pacbio.bsky.social has now oficially adopted polymerase C (KOD Xtreme™ Hot Start DNA polymerase) in their new Ampli-Fi input protocol:
www.pacb.com/blog/new-amp...

New Ampli-Fi ultra-low-input protocol will support HiFi sequencing from as little as 1 ng of DNA - PacBio

The Ampli-Fi protocol is a new workflow that will enable HiFi sequencing from as little as 1 ng of genomic DNA.

www.pacb.com

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Bernhard Bein @bernhardbein.bsky.social · Feb 10

Applying polymerase A/B and C read amplification to two mollusc and one arthropod sample, we saw that assembly contiguity was either higher or comparable with polymerase C reads, and assemblies were always more contigous when combining all libraries, probably due to complementary read drop-outs.

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Bernhard Bein @bernhardbein.bsky.social · Feb 10

Combining reads of polymerase A/B and C with HiC reads, we were able to assemble the maned sloth genome to chromosome level with a contig N50 of ~4.75 Mb, a 10x increase compared to polymerase A/B reads alone.

The assemblies 3.1 Gb size also surpasses the previous 500 Mb protocol size limit.

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Bernhard Bein @bernhardbein.bsky.social · Feb 10

We then used a different polymerase "C" to repeat amplification and sequencing, increasing contig N50 and compleasm/TOGA gene completness dramatically.

Aligning reads of B. torquatus to another sloth species, we saw obvious read drop-outs that polymerase C reads could cover:

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Bernhard Bein @bernhardbein.bsky.social · Feb 10

We therefore switched to the ultra-low input protocol, which contains a PCR amplification step of input DNA, employing two different polymerases we call A/B.

This way, we could sequence the maned sloth Bradypus torquatus to a coverage of 45X.

However, contig N50 of the assembly was below 1 Mb:

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